Gene Set Enrichment For ChIP-seq Peak Data
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Documentation for package ‘chipenrich’ version 2.32.0
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| assign_peaks | Assign peak midpoints to defined gene loci. |
| assign_peak_segments | Assign whole peaks to all overlapping defined gene loci. |
| broadenrich | Run Broad-Enrich on broad genomic regions |
| calc_peak_gene_overlap | Add peak overlap and ratio to result of 'num_peaks_per_gene()' |
| chipenrich | Run ChIP-Enrich on narrow genomic regions |
| chipenrich_package | chipenrich: Gene Set Enrichment For ChIP-seq Peak Data and Other Genomic Regions |
| filter_genesets | Function to filter genesets by locus definition and size |
| genome_to_organism | Get the correct organism code based on genome |
| genome_to_orgdb | Get Entrez ID to gene symbol mappings for custom locus definitions |
| get_test_method | Get the test function name from the method name |
| hybridenrich | Running Hybrid test, either from scratch or using two results files |
| load_peaks | Convert a BEDX+Y data.frame and into GRanges |
| num_peaks_per_gene | Aggregate peak assignments over the 'gene_id' column |
| peaks2genes | Run the test process up to, but not including the enrichment tests. |
| plot_chipenrich_spline | QC plot for ChIP-Enrich |
| plot_dist_to_tss | Plot histogram of distance from peak to nearest TSS |
| plot_gene_coverage | QC plot for Broad-Enrich |
| plot_polyenrich_spline | QC plot for Poly-Enrich |
| polyenrich | Run Poly-Enrich on narrow genomic regions |
| postprocess_peak_grs | A helper function to post-process peak GRanges |
| post_process_enrichments | Post process the 'data.frame' of enrichment results |
| proxReg | Run Proximity Regulation test on a set of narrow genomic regions |
| read_bed | Read files containing peaks or genomic regions |
| read_geneset | Function to read custom gene sets from file |
| read_ldef | Function to read custom locus definition from file |
| read_mappa | Function to read custom mappability files |
| recode_peaks | Recode a vector of number of peaks to binary based on threshold |
| reset_ncores_for_windows | Reset n_cores for Windows |
| setup_genesets | Function to setup genesets |
| setup_locusdef | Function to setup locus definitions |
| setup_mappa | Function to setup mappability |
| supported_genesets | Display supported genesets for gene set enrichment. |
| supported_genomes | Display supported genomes. |
| supported_locusdefs | Display supported locus definitions |
| supported_methods | Display supported gene set enrichment methods. |
| supported_read_lengths | Display supported read lengths for mappability |